Array design and comparative hybridization principle. The Pseudomonas aeruginosa Tiling Array (PATA1) includes ~215000 DNA oligonucleotide probes of 25 bp (black bars). Placed with variable probe spacing (24 – 34 bp) these probes cover 85.9% of the PAO1 genome leaving gaps of up to 9 bp (average ~4). For comparative hybridization, labeled DNA fragments of a reference strain (dark green) and the test strain (light green) were hybridized in parallel to separate PATA1 arrays. Signal ratios were calculated for each oligonucleotide as log2 ratio of test versus reference signal and can e.g. be visualized by the Integrated Genome Browser (IGB). Genetic variations lead to mismatches of sample and probe DNA and hence to a decrease in signal ratio.